package phylogenetics

Phylogenetics

This library provides algorithms and datastructures to perform inferences in molecular evolution. It features:

• typed representation of DNA/amino-acid/codon alphabets

• rate matrices and probability transition matrices for various evolution models (JC69, K80, GTR, Mutsel)

• site-independent Gillespie simulators

• a simulator for gapped alignments under the TKF91 model

• a tree simulator under the birth-death model

• parsers for Newick, NHX and phylip formats

• a GSL-based implementation of the pruning algorithm, with underflow avoidance

Installation

Using opam, simply type

opam install phylogenetics

to install the library, or:

opam pin add -y phylogenetics --dev-repo

to get the current development version.